Genome Analysis Toolkit

Variant Discovery in High-Throughput Sequencing Data

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Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery
and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size.
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Category
Copy Number Variant Discovery

Overview

This is a relatively naive caller that takes the modeled-segments output of ModelSegments and
performs a simple statistical test on the segmented log2 copy ratios to call amplifications and deletions,
given a specified range for determining copy-number neutral segments. This caller is
based on the calling functionality of
ReCapSeg.

If provided ModelSegments results that incorporate allele-fraction data, i.e. data with presumably improved segmentation,
the statistical test performed by CallCopyRatioSegments ignores the modeled minor-allele fractions when making calls.

Input

Copy-ratio-segments .cr.seg file from ModelSegments.
This is a tab-separated values (TSV) file with a SAM-style header containing a read group sample name, a sequence dictionary,
a row specifying the column headers contained in CopyRatioSegmentCollection.CopyRatioSegmentTableColumn,
and the corresponding entry rows.

Output

Called copy-ratio-segments file.
This is a tab-separated values (TSV) file with a SAM-style header containing a read group sample name, a sequence dictionary,
a row specifying the column headers contained in CalledCopyRatioSegmentCollection.CalledCopyRatioSegmentTableColumn,
and the corresponding entry rows.

Usage example

gatk CallCopyRatioSegments \
-I tumor.cr.seg \
-O tumor.called.seg

CallCopyRatioSegments specific arguments

This table summarizes the command-line arguments that are specific to this tool. For more details on each argument, see the list further down below the table or click on an argument name to jump directly to that entry in the list.

Threshold on z-score of non-log2 copy ratio used for determining outlier copy-neutral segments. If non-log2 copy ratio z-score is above this threshold for a copy-neutral segment, it is considered an outlier and not used in the calculation of the length-weighted mean and standard deviation used for calling.

Threshold on z-score of non-log2 copy ratio used for determining outlier copy-neutral segments. If non-log2 copy ratio z-score is above this threshold for a copy-neutral segment, it is considered an outlier and not used in the calculation of the length-weighted mean and standard deviation used for calling.